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<td valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.na</strong></big></big> (28 February 2006)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/user/yhuang/pdb2pqr/trunk/pdb2pqr/src/na.py">/user/yhuang/pdb2pqr/trunk/pdb2pqr/src/na.py</a></font></td></tr></table>
    <p><tt><a href="#Nucleic">Nucleic</a>&nbsp;Acid&nbsp;Structures&nbsp;for&nbsp;PDB2PQR<br>
&nbsp;<br>
This&nbsp;module&nbsp;contains&nbsp;the&nbsp;base&nbsp;nucleic&nbsp;acid&nbsp;structures&nbsp;for<br>
pdb2pqr.<br>
&nbsp;<br>
----------------------------<br>
&nbsp;<br>
PDB2PQR&nbsp;--&nbsp;An&nbsp;automated&nbsp;pipeline&nbsp;for&nbsp;the&nbsp;setup,&nbsp;execution,&nbsp;and&nbsp;analysis&nbsp;of<br>
Poisson-Boltzmann&nbsp;electrostatics&nbsp;calculations<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Copyright&nbsp;(c)&nbsp;2002-2010,&nbsp;Jens&nbsp;Erik&nbsp;Nielsen,&nbsp;University&nbsp;College&nbsp;Dublin;&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Nathan&nbsp;<a href="#A">A</a>.&nbsp;Baker,&nbsp;Washington&nbsp;University&nbsp;in&nbsp;St.&nbsp;Louis;&nbsp;Paul&nbsp;Czodrowski&nbsp;&amp;&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Gerhard&nbsp;Klebe,&nbsp;University&nbsp;of&nbsp;Marburg<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;All&nbsp;rights&nbsp;reserved.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Redistribution&nbsp;and&nbsp;use&nbsp;in&nbsp;source&nbsp;and&nbsp;binary&nbsp;forms,&nbsp;with&nbsp;or&nbsp;without&nbsp;modification,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;are&nbsp;permitted&nbsp;provided&nbsp;that&nbsp;the&nbsp;following&nbsp;conditions&nbsp;are&nbsp;met:<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;of&nbsp;source&nbsp;code&nbsp;must&nbsp;retain&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;in&nbsp;binary&nbsp;form&nbsp;must&nbsp;reproduce&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer&nbsp;in&nbsp;the&nbsp;documentation&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;and/or&nbsp;other&nbsp;materials&nbsp;provided&nbsp;with&nbsp;the&nbsp;distribution.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Neither&nbsp;the&nbsp;names&nbsp;of&nbsp;University&nbsp;College&nbsp;Dublin,&nbsp;Washington&nbsp;University&nbsp;in&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;St.&nbsp;Louis,&nbsp;or&nbsp;University&nbsp;of&nbsp;Marburg&nbsp;nor&nbsp;the&nbsp;names&nbsp;of&nbsp;its&nbsp;contributors&nbsp;may&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;used&nbsp;to&nbsp;endorse&nbsp;or&nbsp;promote&nbsp;products&nbsp;derived&nbsp;from&nbsp;this&nbsp;software&nbsp;without&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;specific&nbsp;prior&nbsp;written&nbsp;permission.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;THIS&nbsp;SOFTWARE&nbsp;IS&nbsp;PROVIDED&nbsp;BY&nbsp;THE&nbsp;COPYRIGHT&nbsp;HOLDERS&nbsp;AND&nbsp;CONTRIBUTORS&nbsp;"AS&nbsp;IS"&nbsp;AND&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;ANY&nbsp;EXPRESS&nbsp;OR&nbsp;IMPLIED&nbsp;WARRANTIES,&nbsp;INCLUDING,&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;THE&nbsp;IMPLIED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;WARRANTIES&nbsp;OF&nbsp;MERCHANTABILITY&nbsp;AND&nbsp;FITNESS&nbsp;FOR&nbsp;<a href="#A">A</a>&nbsp;PARTICULAR&nbsp;PURPOSE&nbsp;ARE&nbsp;DISCLAIMED.&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;IN&nbsp;NO&nbsp;EVENT&nbsp;SHALL&nbsp;THE&nbsp;COPYRIGHT&nbsp;OWNER&nbsp;OR&nbsp;CONTRIBUTORS&nbsp;BE&nbsp;LIABLE&nbsp;FOR&nbsp;ANY&nbsp;DIRECT,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;INDIRECT,&nbsp;INCIDENTAL,&nbsp;SPECIAL,&nbsp;EXEMPLARY,&nbsp;OR&nbsp;CONSEQUENTIAL&nbsp;DAMAGES&nbsp;(INCLUDING,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;PROCUREMENT&nbsp;OF&nbsp;SUBSTITUTE&nbsp;GOODS&nbsp;OR&nbsp;SERVICES;&nbsp;LOSS&nbsp;OF&nbsp;USE,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;DATA,&nbsp;OR&nbsp;PROFITS;&nbsp;OR&nbsp;BUSINESS&nbsp;INTERRUPTION)&nbsp;HOWEVER&nbsp;CAUSED&nbsp;AND&nbsp;ON&nbsp;ANY&nbsp;THEORY&nbsp;OF&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;LIABILITY,&nbsp;WHETHER&nbsp;IN&nbsp;CONTRACT,&nbsp;STRICT&nbsp;LIABILITY,&nbsp;OR&nbsp;TORT&nbsp;(INCLUDING&nbsp;NEGLIGENCE&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OR&nbsp;OTHERWISE)&nbsp;ARISING&nbsp;IN&nbsp;ANY&nbsp;WAY&nbsp;OUT&nbsp;OF&nbsp;THE&nbsp;USE&nbsp;OF&nbsp;THIS&nbsp;SOFTWARE,&nbsp;EVEN&nbsp;IF&nbsp;ADVISED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OF&nbsp;THE&nbsp;POSSIBILITY&nbsp;OF&nbsp;SUCH&nbsp;DAMAGE.<br>
&nbsp;<br>
----------------------------</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="copy.html">copy</a><br>
<a href="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
<a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
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<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.structures.html#Residue">src.structures.Residue</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.na.html#Nucleic">Nucleic</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.na.html#A">A</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#ADE">ADE</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#C">C</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#CYT">CYT</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#G">G</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#GUA">GUA</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#T">T</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#THY">THY</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#U">U</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.na.html#URA">URA</a>
</font></dt></dl>
</dd>
</dl>
</dd>
</dl>
 <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="A">class <strong>A</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Adenosine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Adenosine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#A">A</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="A-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="A-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="A-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="A-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="A-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#A-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="A-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="A-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="A-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="A-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="A-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="A-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="A-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="A-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="A-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="A-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="A-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="A-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="A-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="A-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="A-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="A-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="A-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="A-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="ADE">class <strong>ADE</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Adenosine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Adenosine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#ADE">ADE</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="ADE-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="ADE-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="ADE-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="ADE-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ADE-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#ADE-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="ADE-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="ADE-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ADE-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ADE-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ADE-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="ADE-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ADE-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="ADE-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ADE-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ADE-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ADE-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ADE-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="ADE-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ADE-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ADE-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="ADE-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ADE-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ADE-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="C">class <strong>C</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Cytidine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Cytidine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#C">C</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="C-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="C-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="C-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="C-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="C-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#C-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="C-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="C-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="C-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="C-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="C-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="C-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="C-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="C-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="C-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="C-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="C-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="C-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="C-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="C-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="C-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="C-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="C-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="C-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="CYT">class <strong>CYT</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Cytidine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Cytidine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#CYT">CYT</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="CYT-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="CYT-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="CYT-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="CYT-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="CYT-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#CYT-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="CYT-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="CYT-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYT-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="CYT-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYT-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="CYT-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="CYT-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="CYT-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="CYT-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYT-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYT-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="CYT-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="CYT-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="CYT-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="CYT-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="CYT-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="CYT-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="CYT-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="G">class <strong>G</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Guanosine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Guanosine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#G">G</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="G-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="G-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="G-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="G-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="G-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#G-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="G-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="G-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="G-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="G-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="G-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="G-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="G-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="G-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="G-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="G-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="G-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="G-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="G-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="G-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="G-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="G-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="G-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="G-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="GUA">class <strong>GUA</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Guanosine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Guanosine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#GUA">GUA</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="GUA-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="GUA-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="GUA-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="GUA-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GUA-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#GUA-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="GUA-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="GUA-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GUA-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GUA-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GUA-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="GUA-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GUA-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="GUA-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GUA-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GUA-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GUA-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GUA-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="GUA-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GUA-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GUA-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="GUA-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GUA-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GUA-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Nucleic">class <strong>Nucleic</strong></a>(<a href="src.structures.html#Residue">src.structures.Residue</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#Nucleic">Nucleic</a>&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;provides&nbsp;standard&nbsp;features&nbsp;of&nbsp;the&nbsp;nucleic&nbsp;acids&nbsp;listed<br>
below<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)<br>
&nbsp;&nbsp;&nbsp;&nbsp;ref:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;reference&nbsp;object&nbsp;for&nbsp;the&nbsp;amino&nbsp;acid.&nbsp;&nbsp;Used&nbsp;to<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;convert&nbsp;from&nbsp;the&nbsp;alternate&nbsp;naming&nbsp;scheme&nbsp;to&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;main&nbsp;naming&nbsp;scheme.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Nucleic-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt></dl>

<dl><dt><a name="Nucleic-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="Nucleic-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Nucleic-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#Nucleic-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="Nucleic-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Adds&nbsp;the&nbsp;termini&nbsp;for&nbsp;all&nbsp;inherited&nbsp;objects</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="Nucleic-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="Nucleic-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Nucleic-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Nucleic-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Nucleic-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="Nucleic-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Nucleic-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="Nucleic-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Nucleic-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Nucleic-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Nucleic-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="Nucleic-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="Nucleic-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Nucleic-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Nucleic-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="Nucleic-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="Nucleic-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Nucleic-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="T">class <strong>T</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Thymine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Thymine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#T">T</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="T-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="T-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.&nbsp;&nbsp;In&nbsp;this&nbsp;case&nbsp;it&nbsp;is<br>
always&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="T-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="T-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="T-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#T-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="T-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="T-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="T-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="T-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="T-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="T-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="T-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="T-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="T-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="T-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="T-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="T-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="T-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="T-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="T-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="T-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="T-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="T-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="THY">class <strong>THY</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Thymine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Thymine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#THY">THY</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="THY-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="THY-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.&nbsp;&nbsp;In&nbsp;this&nbsp;case&nbsp;it&nbsp;is<br>
always&nbsp;DNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="THY-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="THY-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="THY-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#THY-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="THY-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="THY-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THY-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="THY-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THY-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="THY-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="THY-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="THY-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="THY-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THY-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THY-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="THY-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="THY-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="THY-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="THY-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="THY-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="THY-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="THY-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="U">class <strong>U</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Uridine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Uridine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#U">U</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="U-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="U-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.&nbsp;&nbsp;In&nbsp;this&nbsp;case&nbsp;it&nbsp;is<br>
always&nbsp;RNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="U-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="U-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="U-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#U-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="U-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="U-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="U-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="U-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="U-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="U-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="U-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="U-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="U-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="U-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="U-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="U-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="U-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="U-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="U-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="U-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="U-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="U-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="URA">class <strong>URA</strong></a>(<a href="src.na.html#Nucleic">Nucleic</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Uridine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Uridine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.na.html#URA">URA</a></dd>
<dd><a href="src.na.html#Nucleic">Nucleic</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="URA-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#A">A</a>&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="URA-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;to&nbsp;distinguish&nbsp;RNA&nbsp;from&nbsp;DNA.&nbsp;&nbsp;In&nbsp;this&nbsp;case&nbsp;it&nbsp;is<br>
always&nbsp;RNA.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.na.html#Nucleic">Nucleic</a>:<br>
<dl><dt><a name="URA-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="URA-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="URA-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Overrides&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;<a href="#URA-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;add&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="URA-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="URA-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="URA-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="URA-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="URA-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="URA-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="URA-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="URA-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="URA-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="URA-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="URA-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="URA-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;<a href="#C">C</a>,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="URA-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="URA-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;<a href="#C">C</a>-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="URA-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="URA-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="URA-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="URA-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<strong>DIHEDRAL</strong> = 57.2958<br>
<strong>SMALL</strong> = 9.9999999999999995e-08<br>
<strong>__author__</strong> = 'Todd Dolinsky'<br>
<strong>__date__</strong> = '28 February 2006'</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Todd&nbsp;Dolinsky</td></tr></table>
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